The interaction between bases on different strands of DNA molecules depends somewhat on the identities of neighboring bases. For example, the melting temperature of an oligonucleotide with the sequence 5′-GGGGGAAAAA-3′ is different than that of 5′-GAGAGAGAGA-3′ even though both contain the exact same number of G-C and A-T base pairs. (The melting temperature is the temperature at which half of the base pairs are broken between the oligonucleotide and its complementary sequence). Therefore, instead of treating a DNA helix as a string of independent base pairs, many thermodynamic algorithms that calculate DNA melting temperatures use the nearest-neighbor model, which treats a DNA helix as a string of interactions between neighboring base pairs. Thus, the sequence GGCTGC contains the nearest neighbors GG, GC, CT and TG and has nearest neighbor frequencies of GG=0.2, GC=0.4, CT=0.2 and TG=0.2. (All sequences written in the standard 5′ è 3′ directionality)
The nearest-neighbor frequencies of a certain double stranded DNA molecule are: AG= 0.15; GT= 0.03; CC= 0.08, and TT= 0.10. In each case the nearest neighbor is written in the 5′?3′ direction. What would be the nearest neighbor frequencies of CT, AC, GG and AA?
